Prime Minister Tony Abbott has issued a stern message to the Indonesian President, saying Australia would ''continue to do what we are entitled to do to secure our borders''.

''Stopping the boats is a matter of sovereignty and President [Susilo Bambang] Yudhoyono of all people ought to understand ... just how seriously countries take their sovereignty. So we will continue to do what we are entitled to do to secure our borders,'' Mr Abbott said.

Happier times: Prime Minister Tony Abbott with Indonesia's President Susilo Bambang Yudhoyono during a visit to Jakarta in September. Mr Abbott has delivered a stern message to the president over Australia's asylum boat policy. Photo: AFP

The Prime Minister made his comments in Davos, Switzerland, where he is attending the three-day World Economic Forum.

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He stressed that President Yudohoyono was ''a great president of Indonesia'' but said he would not be deterred in his mission to ''stop the boats'', despite the diplomatic tensions being caused by the aggressive policies.

''And again I reiterate: the way is shut for the people smugglers and their clients, or would-be clients as far as I am concerned. No illegal boats can expect to get to Australia. Simple as that,'' Mr Abbott said.

President Yudhoyono is still considering how to respond to Australia's apology for violating Indonesia's sovereignty while dealing with asylum seeker boats on the high seas, after the Abbott government announced on Friday that navy and customs vessels carrying out border protection operations had strayed into Indonesian territory.

Jakarta demanded a halt to the operations and vowed to boost naval patrols to its south. including with an extra frigate, and insisted on its ''right to protect its sovereignty and territorial integrity''.

Customs and Defence have started a review into the incursion, with a report due in a few weeks, although this may not be made public.

The Australia-Indonesia relationship has been increasingly fraught since it was revealed recently that Australian spies had been monitoring the phones of the Indonesian president, his wife and confidants.

Mr Abbott is facing further controversies with his asylum seeker policy, after the ABC reported on Wednesday that it had obtained video footage of asylum seekers being treated for burns that Indonesian police allege were inflicted by the Australian Navy.

Immigration Minister Scott Morrison and Lieutenant General Angus Campbell, the commander of the federal government’s military-led border protection policy, have strongly and repeatedly denied any wrongdoing by the navy.

Australian Human Rights Commission president Gillian Triggs has reiterated her calls for all asylum seekers on Nauru and Manus Island to be returned to Australia.

Professor Triggs said the commission was particularly concerned about asylum seekers detained on Nauru and who had been charged with riot offences.

"As the commission has continued to point out, Australia cannot avoid its international human rights obligations by transferring asylum seekers to third countries and may remain liable for the consequences of doing so," she said.

"Australia should ensure that adequate safeguards are in place in those countries at all times, including the application of the rule of law."

Asked in Davos if he was still confident about sending asylum seekers to the tiny island nation, Mr Abbott said: ''Well, we are sending people who arrive illegally by boat to Nauru, as part of the range of measures that we have put in place which, just at the moment, seems to be very effective in stopping the boats. Nauru remains an important part of a range of policies, which are proving to be much more effective than the policies of former government in stopping the boats.''

Mr Abbott is also facing questions on broader human rights concerns.

The independent organisation Human Rights Watch, has released its 2014 World Report, in which it strongly criticises the Australian government for its harsh new asylum seeker policies.

''Australia has a strong record protecting civil and political rights, but has damaged its record and its potential to be a regional human rights leader by persistently undercutting refugee protections,'' the report states.

''In 2013, successive Australian governments continued to engage in scare-mongering politics at the expense of the rights of asylum seekers and refugees.''

The damning report also condemns the Australian government for being ''increasingly unwilling to publicly raise human rights abuses in countries with which it has strong trade or security ties, fearing that doing so would harm its relations with Asian governments''.

Australia's human rights watchdog is also setting up an inquiry into the detention of child asylum seekers.

Ms Triggs said about 1000 children are in immigration detention.

''We're not getting the level of information we used to get,'' she told ABC radio on Wednesday, indicating she would announce details of an inquiry soon.

Ms Triggs said as a matter of law children should not be detained unless as a last resort.

''We're concerned holding children, beyond what is necessary for health checks and identity checks . . . to hold them for months or even years does really raise the question of Australia's compliance with its international obligations.''

Speaking to journalists at Davos, Mr Abbott said he was ''looking forward'' to his next meeting with President Yudhoyono and hoped the meeting would happen ''sooner rather than later''.

''As far as I am concerned, I want nothing but good in the relationship between Australia and Indonesia.''

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